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This repository has been archived by the owner on Nov 2, 2022. It is now read-only.
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(archived) A simple chemical structure graph modeling, drawing and analysis toolkit

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mojaie/chorus

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Chorus

Chorus is a simple chemical structure modeling toolkit.

Installation

PyPI

pip3 install chorus

Poetry

git clone https://github.com/mojaie/chorus.git
cd chorus
poetry install
poetry run make build
cd ../project
poetry add ../chorus

Anaconda

Distributing conda package is work in progress.

conda upgrade -n root conda
conda install -n root conda-build

conda skeleton pypi chorus
conda build chorus
conda install --use-local chorus

Features

  • Structure image export (PNG)

  • Structure image export (SVG)

  • Import from/export to .sdf, .mol

  • Import from/export to RDKit molecule

  • Molecular property calculation (MW, Chemical formula)

  • Descriptors

    • H-bond donor/acceptor
    • Wildman-Crippen logP
    • Aromaticity
  • Molecule graph topology (ring, scaffold, connectivity)

  • Sub(super)structure search

  • MCS with diameter restriction (MCS-DR) and graph-based local similarity (GLS)

Features (WIP)

  • Functional group descriptors
  • Markush structue
  • SMILES and 2D coordinate generation

Features (will never be implemented)

  • Python 2 compatibility
  • Fingerprint similarity
  • And many of the features already available in RDKit

API Documentation

https://chorus-docs.readthedocs.io/

License

MIT license

See chorus/resources/README.md for license details of sample dataset resources.

Copyright

(C) 2014-2018 Seiji Matsuoka